Update species data location

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+omit = *test/*
+branch = True

.coveralls.yml

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+service_name: travis-ci
+repo_token: Pk8rldcpUmf4b8ITeoa7XBYHiAc3LNXlc

.gitignore

@@ -4,4 +4,12 @@ build
 dist
 .idea*
 .idea/*
-*DS_store
+*DS_store
+
+virtualenv
+
+# emacs
+*~
+.coverage
+.ipynb_checkpoints
+_build

.travis.yml

@@ -0,0 +1,65 @@
+language: python
+python:
+#  - "2.6"
+  - "2.7"
+#  - "3.3"
+#  - "3.4"
+
+# Set up our virtualenv
+before_install:
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.4.2-Linux-x86_64.sh -O miniconda.sh; fi
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then export PATH=~/miniconda/bin:$PATH; else export PATH=~/miniconda3/bin/:$PATH; fi
+  - conda update --yes conda
+# Set up coveralls
+  - export COVERALLS_SERVICE_NAME=travis-ci
+  - export COVERALLS_REPO_TOKEN=Pk8rldcpUmf4b8ITeoa7XBYHiAc3LNXlc
+
+# command to install dependencies
+install:
+  - conda create -n testenv --yes python=$TRAVIS_PYTHON_VERSION
+  - source activate testenv
+  # install as much as we can via conda
+  - conda install --yes pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml
+  # Install the rest via pip (brewer2mpl, gspread, seaborn, etc)
+  - pip install -r requirements.txt
+  - pip install pep8
+  - pip install https://github.com/dcramer/pyflakes/tarball/master
+  - pip install coveralls
+
+before_script:
+  - git config --global user.email "olga.botvinnik@gmail.com"
+  - git config --global user.name "olgabot"
+  - git config --global push.default simple
+  - export REPO_URL_GITHUB="https://$GH_TOKEN@github.com/$GH_REPO.git"
+  - . ./.travis/setup.sh # make any change needed for setup.sh
+  - echo $DEPLOY_HTML_DIR
+
+# command to run tests
+script:
+  - make coverage
+  - make lint
+  - make pep8
+
+after_script:
+  - coveralls
+  # For building the docs
+  - MASTER=master
+  - if [[ $TRAVIS_BRANCH == v*.*.* ]] ; then export DEPLOY_HTML_DIR=docs ; fi
+  - if [[ $TRAVIS_BRANCH == "$MASTER" ]] ; then export DEPLOY_HTML_DIR=docs-dev ; fi
+  - if [[ $TRAVIS_BRANCH == v*.*.* ]] || [[ $TRAVIS_BRANCH == "$MASTER" ]] ; then sudo apt-get install pandoc; pip install sphinx numpydoc sphinx_bootstrap_theme runipy; sudo pip install -r doc/requirements.txt --use-mirrors; cd doc ; make setup_gh_pages ; make generate ; make deploy ; fi
+
+# For slack notifications
+notifications:
+  slack:
+    rooms:
+    - yeolab:HxLwrd5FGhZQ8SyBD9Fvh3dn#flotilla
+
+env:
+  global:
+    - GH_REPO="YeoLab/flotilla" #change this to your right project
+    - secure: N8LIn+ZtvaL+j9uHJFRtTWHbJtLk47r+7PUaSPapmpRPkqD4zClwC1+xVrfRXYiTWLVmCMfbcOAjQmZR8OjL8TKD4yGPzXAS5yb9QUhlMBf2is7CECIZQcQ/kht4KGKF72QoRY4r/Eh4NKhayBUWwZmHXd5zIKn8C/irvr+6LBI=
+
+  # configure the right travis-ci secure key, see sphinx-deployment/README for more details
+  #- secure: im3gWbsEF135C0jKlOIRJUa1tgtsCAaqwGDSpzwe/fnTosqystNE+mhvFfERmy1K4qRg0cbRYGd8L6pP/V7RR3GMqFX4h5wexZeKsCN895S0d7QIWUmw2yJ3+mvk/g+E6q56tORzhKzKVRef5VWkk84EOKrZ/KIeoVpKVAlVR1s=

.travis/setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+#setup travis-ci configuration basing one the being-built branch
+
+if [[ $TRAVIS_BRANCH == 'master' ]] ; then
+    export DEPLOY_HTML_DIR=docs
+elif [[ $TRAVIS_BRANCH == 'develop' ]] ; then
+    export DEPLOY_HTML_DIR=docs/develop
+elif [[ $TRAVIS_BRANCH =~ ^v[0-9.]+$ ]]; then
+    export DEPLOY_HTML_DIR=docs/${TRAVIS_BRANCH:1}
+else
+    export DEPLOY_HTML_DIR=docs/$TRAVIS_BRANCH
+fi

CONTRIBUTING.md

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+
+For developers
+==============
+
+Please put ALL import statements at the top of the `*.py` file (potentially underneath docstrings, of course).
+The only exception is if a package is not listed in `requirements.txt`,then a "function-only" import may be allowed.
+If this doesn't make sense to you, just put the import at the top of the file.
+
+
+Install in development mode
+---------------------------
+
+First clone the repository,
+
+    git clone git@github.com:YeoLab/flotilla
+
+Change directories to the flotilla directory you just made,
+
+    cd flotilla
+
+Now install via `pip` in "editable" mode, aka "develop" mode:
+
+    pip install -e .
+
+Git branching
+-------------
+
+We use the [GitHub-Flow](http://scottchacon.com/2011/08/31/github-flow.html) model.
+
+To contribute:
+
+1.    Make a branch off of the master.
+
+2.    Commit updates exclusively to your branch.
+
+3.    When changes on that branch are finished, open a [pull request](https://help.github.com/articles/using-pull-requests/).
+
+4.    Once someone has reviewed and approved of the changes on your branch, you should immediately merge your branch into the master.
+
+Naming conventions
+------------------
+
+When in doubt, please defer to [Python Enhancement Proposal 8 (aka [PEP8]
+(http://legacy.python.org/dev/peps/pep-0008/)) and the [Zen of Python]
+(http://legacy.python.org/dev/peps/pep-0020/)
+
+* Classes are `CamelCase`, e.g.:  `BaseData` and `PCAViz`
+* Functions are `lower_case_with_underscores`, e.g. `go_enrichment` and
+`binify`
+* Explicit is better than implicit
+
+
+Docstring conventions
+---------------------
+
+We will attempt to stick to the [`numpy` docstring specification](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt) (aka
+"`numpydoc`").
+
+To make this easier, I use ["Live Templates" in PyCharm]
+(http://peter-hoffmann.com/2010/python-live-templates-for-pycharm.html),
+check out the instructions [here](https://github.com/YeoLab/PyCharm-Python-Templates) for how to install and use them.
+
+Testing
+-------
+
+In the source directory (wherever you cloned `flotilla` to that has this README.md file), do:
+
+    make test
+
+This will run the unit test suite.
+
+### Coverage
+
+To check coverage of the test suite, run
+
+    make coverage
+
+in the source directory.
+
+
+PEP8 Conventions
+----------------
+
+To run `pep8` and `pyflakes` over the code, make sure you have [this fork]
+(pip install https://github.com/dcramer/pyflakes/tarball/master) of
+`pyflakes` installed (e.g. via `pip install https://github
+.com/dcramer/pyflakes/tarball/master`) and run:
+
+    make lint
+
+Pull Request Checklist
+----------------------
+
+When you make a pull request, please copy this text into your first message 
+of the pull request, which will create a checklist, which should be completed 
+before the pull request is merged.
+
+```
+- [ ] Is it mergable?
+- [ ] Did it pass the tests?
+- [ ] If it introduces new functionality in is it tested?
+  Check for code coverage. To run code coverage on only the file you changed,
+  for example `flotilla/compute/splicing.py`, use this command: 
+  `py.test --cov flotilla/compute/splicing.py --cov-report term-missing flotilla/test/compute/test_splicing.py`
+  which will show you which lines aren't covered by the tests.
+- [ ] Do the new functions have descriptive 
+  [numpydoc](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)
+  style docstrings?
+- [ ] If it adds a new feature, is it documented as an IPython Notebook in 
+  `examples/`, and is that notebook added to `doc/tutorial.rst`?
+- [ ] If it adds a new plot, is it documented in the gallery, as a `.py` file 
+  in `examples/`?
+- [ ] Is it well formatted? Look at `make pep8` and `make lint` output
+- [ ] Is it documented in the doc/releases/?
+- [ ] Was a spellchecker run on the source code and documentation after
+  changes were made?
+```
+
+Note: This checklist was heavily borrowed from the [khmer](https://khmer.readthedocs.org/en/latest/dev/coding-guidelines-and-review.html#checklist) project.

INSTALL.md

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+Docker Installation Instructions
+================================
+
+[Docker](https://www.docker.com/whatisdocker/) is the preferred method to obtain the most up-to-date
+version of `flotilla`. Every change we make to the source code triggers a new build of a virtual
+ machine that contains flotilla and all its dependencies.
+
+Please follow instructions [here](docker/docker_instructions.md) to get, install, and run the `flotilla` image.
+
+
+
+OS X Installation instructions
+==============================
+
+The following steps have been tested on a clean install of Mavericks 10.9.4.
+
+All others must fend for themselves to install matplotlib, scipy and their third-party dependencies.
+
+ *This part only needs to be done once*
+
+ * [Install anaconda](https://store.continuum.io/cshop/anaconda/)
+ * [Install Xcode (this can take an hour)](https://itunes.apple.com/us/app/xcode/id497799835?mt=12)
+ * Open Xcode and agree to terms and services (it is very important to read them thoroughly)
+ * Install [homebrew](http://brew.sh/)
+
+
+    `ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"`
+
+
+ * Install freetype:
+
+
+    `brew install freetype`
+
+
+ * Install heavy packages (this can take an hour or more)
+
+```
+conda install pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml`
+```
+
+ * Create a virtual environment
+```
+conda create -n flotilla_env pip numpy scipy cython matplotlib nose six scikit-learn ipython networkx pandas tornado statsmodels setuptools pytest pyzmq jinja2 pyyaml`
+```
+
+ * Switch to virtual environment
+
+
+    `source activate flotilla_env`
+
+
+ * Install flotilla and its dependencies (this can take a few minutes):
+
+
+    `pip install git+https://github.com/YeoLab/flotilla.git`
+
+
+ * Create a scratch space for your work
+
+
+    `mkdir ~/flotilla_scratch`
+
+
+ * Make a place to store flotilla projects
+
+
+    `mkdir ~/flotilla_projects`
+
+
+ * Go back to the real world
+
+    `source deactivate`
+
+
+
+ * switch to virtual environment
+
+
+    `source activate flotilla_env`
+
+
+ * start an ipython notebook:
+
+
+    `ipython notebook --notebook-dir=~/flotilla_scratch`
+
+
+ * create a new notebook by clicking `New Notebook`
+ * rename your notebook from "Untitled" to something more informative by clicking the title panel.

LICENSE

@@ -1,21 +1,37 @@
-The MIT License (MIT)
+UC Copyright Notice
 
-Copyright (c) 2014, Michael Lovci, Olga Botvinnik, Gene Yeo
+This software is Copyright (C) 2014 The Regents of the University of California. All Rights Reserved.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Permission to copy, modify, and distribute this software and its documentation for educational,
+research and non-profit purposes, without fee, and without a written agreement is hereby granted,
+provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+Permission to make commercial use of this software may be obtained by contacting:
+Technology Transfer Office
+9500 Gilman Drive, Mail Code 0910
+University of California
+La Jolla, CA 92093-0910
+(858) 534-5815
+invent@ucsd.edu
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+This software program and documentation are copyrighted by The Regents of the
+University of California. The software program and documentation are supplied
+"as is", without any accompanying services from The Regents. The Regents does
+not warrant that the operation of the program will be uninterrupted or
+error-free. The end-user understands that the program was developed for
+research purposes and is advised not to rely exclusively on the program for
+any reason.
+
+IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO
+ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR
+CONSEQUENTIAL DAMAGES, INCLDING LOST PROFITS, ARISING
+OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION,
+EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE. THE UNIVERSITY OF
+CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
+AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO
+PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
+MODIFICATIONS.

Makefile

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+export SHELL := /bin/bash
+
+test:
+	cp testing/matplotlibrc .
+	py.test
+	rm matplotlibrc
+
+coverage:
+	cp testing/matplotlibrc .
+	py.test --durations=20 --cov flotilla --cov-report term-missing flotilla/test/
+	rm matplotlibrc
+
+lint:
+	pyflakes flotilla
+
+pep8:
+	pep8 flotilla